The comment about "not controlling for O2" is referring to the fact that the human body can't directly detect blood oxygen levels, and only infers them from blood CO2 levels. So if something's going wrong with the oxygen absorption process but the CO2 exhalation process is still fine, that would explain why patients have dangerously low blood oxygen but aren't panting or otherwise showing respiratory distress.

(Incidentally this is also why it's really dangerous to hyperventilate before free diving, because you can put your O2 / CO2 ratio out of whack which can cause you to black out without warning while under water.)